Here are some ideas:
1.) Distinguish Disabled from Destroyed. A module is disabled at 25% health and destroyed at 0%. Therefore, if the body module, or the module holding the cockpit is disabled, the mecha is disabled but not destroyed. For added fun, destroyed modules can not be repaired and the player has to buy a replacement.
2.) Require additional steps to salvage. Instead of automatically recovering mecha that are recoverable, a recover/salvage dialog window opens up after the battle. If salvage was allowed, the player can select the equipment to recover, and if near a friendly station, can pay to have a "recovery team" come by and recover mecha that require a new cockpit, and salvage mecha that were disabled but not destroyed. A mecha that had its pilot killed could be recovered for free if the player's team had a dismounted mecha pilot (assumes that they are a passenger in one of the other mecha). This method also has the benefit of integrating well with Ships (i.e. recovery and salvage components) when they are implemented. Conversely, enemies would only be allowed to salvage if they were within range of their "base".
3.) Strip and run. If the player ejects, the mecha is left dead in space. Since the pirates need to get back to their hideout before the cops arrive, dragging a heavy mecha around isn't an option. However, there they can yank off everything that isn't bolted down (i.e. external armor and mounted weapons and thrusters) and clean out the hold. Afterwards, the player could claim what's left of their mecha. More advanced pirates might even ransom more expensive mecha, threatening to destroy them if the player doesn't cough up the credits. If this were to be implemented, I would recommend making Mecha weapon and armor shops more common, and low end weapons cheaper.
4.) Dangerous ejections. If the module holding the mecha's cockpit is destroyed, the pilot is forced to make a "emergency ejection" roll. The roll would be athletics against something like 10 + the DC of the attacker's weapon - the cockpit's armor rating - 5 for head mounted cockpits. Every point the roll is missed by randomly increases the DC or BV of an attack against the pilot.